Phylogenomic Analysis and Dynamic Evolution of Chloroplast Genomes of Clematis nannophylla

Abstract

Background Clematis nannophylla is a small perennial shrub of Clematis with a high ecological, ornamental, and medicinal value and is distributed in the arid and semi-arid areas of northwest China. In this study, we successfully determined the complete chloroplast genome of C. nannophylla and reconstructed a phylogenetic tree of Clematis.Results The chloroplast genome of C. nannophylla was 159801 bp in length, including a large single-copy (LSC,79526bp), a small single-copy (SSC,18185bp), and a pair of reverse repeats(IRa and IRb,31045bp). The C. nannophylla cp genome contained 133 unique genes, including 89 protein-coding genes, 36 tRNA genes, and eight rRNA genes. In addition, 61 codons and 66 simple repeat sequences (SSR) were identified, of which 50 dispersed repeats (including 22 forward, 21 palindromic and 7 reverse) and 24 tandem repeats were found in C. nannophylla. Many of the dispersed and tandem repeats were between 20–30 bp and 10–20 bp, respectively. The chloroplast genome of C. nannophylla was relatively conserved, especially in the IR region, where no inversion or rearrangement was observed. The six regions with the largest variations were trnF-ndhJ, ndhE-ndhG, ndhF-rpl32, ccsA-ndhD, ccsA, and ndhD (Pi > 0.008), which were distributed in the LSCS and SSCs. A comparison of gene selection pressures indicated that purification was the main mode of selection for maintaining important biological functions in the chloroplast genome of C. nannophylla. However, to adapt to the living environment, ycf1 was positively selected (C. nannophylla and C. florida). Phylogenetic analysis showed that C. nannophylla was more closely related to C. fruticosa and C. songorica.Conclusions Our analysis of the C. nannophylla cp genome provides reference data for molecular marker development, phylogenetic analysis, population studies, and chloroplast genome processes, as well as for better exploitation and utilisation of C. nannophylla.